I think the reactor scene was a case of Bob Orci trying to get too cute. "Oooh, let's redo the Spock death scene from TWOK.....but in reverse, wouldn't that be so Hitchcock-like of us". That totally ruined any poignancy moment for me. The whole time instead of focusing on Kirk's moment of mortality I was focusing on 'they didn't just seriously do that.' Then Spock screaming Khan a la Shatner (never try to out-Shat the Shatner). My eyes rolled so far back with that one that I swear I could see out my optic nerve. I always thought even Abrams thought that was too much because that scene quickly cuts to the next (Spock screams--"KHAAAAAA--" cut away to Vengeance flying into the atmosphere). And then, of course, Kirk is miraculously brought back by magic blood (that's a whole other issue I have but I'll save that for another day). Now, I get that it'd be difficult to really kill off one of your main characters. But honestly, you want to shock people, do the unexpected for real.
I'd say I probably liked 80% of STID. The Khan reveal took it down a few notches, not the least because Cumberbatch reminded me absolutely nothing of Khan, zilch (kind of a shame because Cumberbatch did a great job as never before seen John Harrison). But the biggest drop for me, and most of that 20% reduction had to do with the blatant TWOK rip off near the end. Things were otherwise going pretty well up to that point.